1GIK

POKEWEED ANTIVIRAL PROTEIN FROM SEEDS


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.243 
  • R-Value Work: 0.183 
  • R-Value Observed: 0.183 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Crystal structure of pokeweed antiviral protein with well-defined sugars from seeds at 1.8 angstrom resolution

Zeng, Z.H.He, X.L.Li, H.M.Hu, Z.Wang, D.C.

(2003) J Struct Biol 141: 171-178

  • DOI: 10.1016/s1047-8477(02)00580-4
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • The crystal structure of pokeweed antiviral protein from seeds of Phytolacca americana (PAP-S) was solved at 1.8A. PAP-S is a one-chain ribosome-inactivating protein (RIP) and distinctively contains three well-defined N-acetylglucosamines, each coval ...

    The crystal structure of pokeweed antiviral protein from seeds of Phytolacca americana (PAP-S) was solved at 1.8A. PAP-S is a one-chain ribosome-inactivating protein (RIP) and distinctively contains three well-defined N-acetylglucosamines, each covalently linked to an asparagine residue at positions, 10, 44, and 255, respectively. The high-resolution structure clearly shows the three mono-sugars to have either an alpha- or a beta-conformation. Two of sugars are located on the same side of the molecule with the active pocket. Except one hydrogen bond, there are no intermolecular interactions between the polypeptide chain and the sugars. Instead the sugar conformations appear to be stabilized by intermolecular interactions. The sugar structure defined at high resolution provides a structural basis for understanding their possible biological activity. The structural comparisons of PAP-S with other PAPs reveal that the major disparity of these homologous molecules is the different charge distribution on the upper right side of the front side near the active pocket. Based on the available structure of the 50S ribosomal subunit, the possible interactions between PAPs and the ribosome are discussed.


    Related Citations: 
    • CRYSTALLIZATION AND PERLIMINARY CRYSTALLOGRAPHIC ANALYSES OF POKEWEED ANTIVIRAL PROTEIN FROM SEEDS
      Li, H.M., Zeng, Z.H., Hu, Z., Wang, D.C.
      (1998) Acta Crystallogr D Biol Crystallogr 54: 137
    • CRYSTAL STRUCTURE OF A POKEWEED ANTIVIRAL PROTEIN FROM SEEDS OF PHYTOLACCA AMERICANA AT 0.25 NM
      Zeng, Z.H., JIN, L., LI, H.M., HU, Z., Wang, D.C.
      (1998) Sci China C Life Sci 41: 413
    • X-ray Structure of a Pokeweed Antiviral Protein, Coded by a New Genomic Clone, at 0.23 nm resolution. A Model Structure Provides a Suitable Electrostatic Field for Substrate Binding
      Ago, H., Kataoka, J., Tsuge, H., Habuka, N., Inagaki, E., Noma, M., Miyano, M.
      (1994) Eur J Biochem 225: 369
    • The 2.5 A Structure of Pokeweed Antiviral Protein
      Monzingo, A.F., Collins, E.J., Erust, S.R., Irvin, J.D., Robertus, J.D.
      (1993) J Mol Biol 233: 705

    Organizational Affiliation

    Center for Molecular Biology, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China.



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
ANTIVIRAL PROTEIN S
A
261Phytolacca americanaMutation(s): 0 
EC: 3.2.2.22
Find proteins for P23339 (Phytolacca americana)
Go to UniProtKB:  P23339
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NAG
Query on NAG

Download CCD File 
A
N-ACETYL-D-GLUCOSAMINE
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
NDG
Query on NDG

Download CCD File 
A
2-(ACETYLAMINO)-2-DEOXY-A-D-GLUCOPYRANOSE
C8 H15 N O6
OVRNDRQMDRJTHS-PVFLNQBWSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.243 
  • R-Value Work: 0.183 
  • R-Value Observed: 0.183 
  • Space Group: I 2 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 84.76α = 90
b = 78.05β = 90
c = 91.57γ = 90
Software Package:
Software NamePurpose
WEISdata scaling
CCP4data reduction
AMoREphasing
X-PLORrefinement
WEISdata reduction
CCP4data scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2003-09-30
    Type: Initial release
  • Version 1.1: 2008-04-26
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Non-polymer description, Version format compliance
  • Version 1.3: 2017-10-04
    Changes: Refinement description